Estimating SARS-CoV-2 Omicron XBB.1.5 Spike-Directed Functional Antibody Levels From an Anti-Receptor Binding Domain Wuhan-Hu-1-Based Commercial Immunoassay Results.

We investigated whether antibody concentrations measured in plasma using the Roche Elecsys® Anti-SARS-CoV-2 S assay (targeting the receptor binding domain, RBD) could estimate levels of Wuhan-Hu-1 and Omicron XBB.1.5 spike-directed antibodies with neutralizing ability (NtAb) or those mediating NK-cell activity.

Almond Grafting for Plum Pox Virus Resistance Triggers Significant Transcriptomic and Epigenetic Shifts in Peaches.

Sharka disease, caused by the plum pox virus (PPV), negatively impacts stone fruit production, resulting in economic losses. It has been demonstrated that grafting the almond ( (Miller) D.A.

Chronology of transcriptome and proteome expression during early Arabidopsis flower development.

The complex gene regulatory landscape underlying early flower development in Arabidopsis has been extensively studied through transcriptome profiling, and gene networks controlling floral organ development have been derived from the analyses of genome wide binding of key transcription factors. In contrast, the dynamic nature of the proteome during the flower development process is much less understood. In this study, we characterized the floral proteome at different stages during early flower development and correlated it with unbiased transcript expression data.

Complete Genomes of DNA Viruses in Fecal Samples from Small Terrestrial Mammals in Spain.

Viromics studies are allowing us to understand not only the enormous diversity of the virosphere, but also the potential threat posed by the emerging viruses. Regarding the latter, the main concern lies in monitoring the presence of RNA viruses, but the zoonotic potential of some DNA viruses, on which we have focused in the present study, should also be highlighted. For this purpose, we analyzed 160 fecal samples from 14 species of small terrestrial mammals, 9 of them belonging to the order .

Immune digital twins for complex human pathologies: applications, limitations, and challenges.

Digital twins represent a key technology for precision health. Medical digital twins consist of computational models that represent the health state of individual patients over time, enabling optimal therapeutics and forecasting patient prognosis. Many health conditions involve the immune system, so it is crucial to include its key features when designing medical digital twins.

Toward understanding grapevine responses to climate change: a multistress and holistic approach.

Recent research has extensively covered the effects of climate change factors, such as elevated CO2, rising temperatures and water deficit, on grapevine (Vitis spp.) biology. However, the assessment of the impacts of multiple climate change-related stresses on this crop remains complex due to the large number of interactive effects among environmental factors and the regulatory mechanisms that underlie these effects.

Chemical activation of ABA signaling in grapevine through the iSB09 and AMF4 ABA receptor agonists enhances water use efficiency.

Grapevine (Vitis vinifera L.) is the world's third most valuable horticultural crop, and the current environmental scenario is massively shifting the grape cultivation landscape. The increase in heatwaves and drought episodes alter fruit ripening, compromise grape yield and vine survival, intensifying the pressure on using limited water resources.

Microviridae bacteriophages influence behavioural hallmarks of food addiction via tryptophan and tyrosine signalling pathways.

Food addiction contributes to the obesity pandemic, but the connection between how the gut microbiome is linked to food addiction remains largely unclear. Here we show that Microviridae bacteriophages, particularly Gokushovirus WZ-2015a, are associated with food addiction and obesity across multiple human cohorts. Further analyses reveal that food addiction and Gokushovirus are linked to serotonin and dopamine metabolism.

Murine colon cancer derived cells exhibit heterogeneous resistance profiles against an oncolytic virus.

Oncolytic virotherapy has shown efficacy in various animal models and a few human cancers. However, there are still significant limitations for the implementation of these therapies. One such limitation is the emergence of cellular resistances, which may appear rapidly considering the high genetic heterogeneity of most tumors.

Quantifying defective and wild-type viruses from high-throughput RNA sequencing.

Motivation: Defective viral genomes (DVGs) are variants of the wild-type (wt) virus that lack the ability to complete autonomously an infectious cycle. However, in the presence of their parental (helper) wt virus, DVGs can interfere with the replication, encapsidation, and spread of functional genomes, acting as a significant selective force in viral evolution. DVGs also affect the host's immune responses and are linked to chronic infections and milder symptoms.

Multiomics of the intestine-liver-adipose axis in multiple studies unveils a consistent link of the gut microbiota and the antiviral response with systemic glucose metabolism.

Background: The microbiota is emerging as a key factor in the predisposition to insulin resistance and obesity.

Objective: To understand the interplay among gut microbiota and insulin sensitivity in multiple tissues.

Design: Integrative multiomics and multitissue approach across six studies, combining euglycaemic clamp measurements (used in four of the six studies) with other measurements of glucose metabolism and insulin resistance (glycated haemoglobin (HbA1c) and fasting glucose).

Probing the orthogonality and robustness of the mammalian RNA-binding protein Musashi-1 in Escherichia coli.

RNA recognition motifs (RRMs) are widespread RNA-binding protein domains in eukaryotes, which represent promising synthetic biology tools due to their compact structure and efficient activity. Yet, their use in prokaryotes is limited and their functionality poorly characterized. Recently, we repurposed a mammalian Musashi protein containing two RRMs as a translation regulator in Escherichia coli.

Low Silver/Copper Exchange in a Copper-Phosphate Enzyme Nanoflower Hybrid Extremely Enhanced Antimicrobial Efficacy against Multidrug Resistant Bacteria.

Infections caused by bacteria that are resistant to many drugs are a major threat to public health in many countries around the world. Here we demonstrate the creation of heterogeneous catalytic nanomaterials with outstanding antimicrobial properties against several superbugs. We have shown that replacing a small amount of copper in a generated copper-phosphate-enzyme nanoflower hybrid with silver drastically increases the antimicrobial capacity of the nanomaterial.

A multispecies study reveals the diversity and potential regulatory role of long noncoding RNAs in cucurbits.

Plant long noncoding RNAs (lncRNAs) exhibit features such as tissue-specific expression, spatiotemporal regulation, and stress responsiveness. Although diverse studies support the regulatory role of lncRNAs in model plants, our knowledge about lncRNAs in crops is limited. We employ a custom pipeline on a dataset of over 1000 RNA-seq samples across nine representative species of the family Cucurbitaceae to predict 91 209 nonredundant lncRNAs.

SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments.

SQANTI-reads leverages SQANTI3, a tool for the analysis of the quality of transcript models, to develop a read-level quality control framework for replicated long-read RNA-seq experiments. The number and distribution of reads, as well as the number and distribution of unique junction chains (transcript splicing patterns), in SQANTI3 structural categories are informative of raw data quality. Multi-sample visualizations of QC metrics are presented by experimental design factors to identify outliers.

The microwave bacteriome: biodiversity of domestic and laboratory microwave ovens.

Microwaves have become an essential part of the modern kitchen, but their potential as a reservoir for bacterial colonization and the microbial composition within them remain largely unexplored. In this study, we investigated the bacterial communities in microwave ovens and compared the microbial composition of domestic microwaves, microwaves used in shared large spaces, and laboratory microwaves, using next-generation sequencing and culturing techniques. The microwave oven bacterial population was dominated by , , , and , similar to the bacterial composition of human skin.

Genetic diversity and cross-species transmissibility of bat-associated picornaviruses from Spain.

Background: Emerging zoonotic diseases arise from cross-species transmission events between wild or domesticated animals and humans, with bats being one of the major reservoirs of zoonotic viruses. Viral metagenomics has led to the discovery of many viruses, but efforts have mainly been focused on some areas of the world and on certain viral families.

Methods: We set out to describe full-length genomes of new picorna-like viruses by collecting feces from hundreds of bats captured in different regions of Spain.

Activation of the yeast Retrograde Response pathway by adaptive laboratory evolution with S-(2-aminoethyl)-L-cysteine reduces ethanol and increases glycerol during winemaking.

Background: Global warming causes an increase in the levels of sugars in grapes and hence in ethanol after wine fermentation. Therefore, alcohol reduction is a major target in modern oenology. Deletion of the MKS1 gene, a negative regulator of the Retrograde Response pathway, in Saccharomyces cerevisiae was reported to increase glycerol and reduce ethanol and acetic acid in wine.

In Vitro and In Silico Anthelmintic Activity of Extracts of and on .

The aim of this study was to assess the anthelmintic activity of and , on a nematode model, to promote their use in the Cameroonian pharmacopoeia for the treatment of helminthiases. One nematode was used, . First, the effect of the extracts on the eggs and larval stages (L1, L2, and L3) of was evaluated, 100 L of extract and 100 L of parasite suspension (containing 50 eggs) were mixed in a 96-well microplate.

Adaptability of the gut microbiota of the German cockroach Blattella germanica to a periodic antibiotic treatment.

High-throughput sequencing studies have shown that diet or antimicrobial treatments impact animal gut microbiota equilibrium. However, properties related to the gut microbial ecosystem stability, such as resilience, resistance, or functional redundancy, must be better understood. To shed light on these ecological processes, we combined advanced statistical methods with 16 S rRNA gene sequencing, functional prediction, and fitness analyses in the gut microbiota of the cockroach Blattella germanica subject to three periodic pulses of the antibiotic (AB) kanamycin (n=512).

DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models.

Bacteriophages (phages) are viruses that infect bacteria. Many of them produce specific enzymes called depolymerases to break down external polysaccharide structures. Accurate annotation and domain identification of these depolymerases are challenging due to their inherent sequence diversity.